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- PDB-4boc: Structure of mitochondrial RNA polymerase elongation complex -

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Basic information

Entry
Database: PDB / ID: 4boc
TitleStructure of mitochondrial RNA polymerase elongation complex
Components
  • 5'-D(*CP*AP*TP*GP*GP*GP*GP*TP*AP*AP*TP*TP*AP*TP *TP*TP*CP*GP*AP*CP*GP*CP*CP*AP*GP*AP*CP*G)-3'
  • 5'-D(*CP*GP*TP*CP*TP*GP*GP*CP*GP*TP*GP*CP*GP*CP *GP*CP*CP*GP*CP*TP*AP*CP*CP*CP*CP*AP*TP*G)-3'
  • 5'-R(*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP)-3'
  • DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIALPolymerase
KeywordsTRANSCRIPTION / RNA POLYMERASE / MITOCHONDRIA / TRANSFERASE / DNA-RNA HYBRID
Function / homology
Function and homology information


Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / transcription initiation at mitochondrial promoter / mitochondrial transcription / DNA primase activity / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / transcription initiation at mitochondrial promoter / mitochondrial transcription / DNA primase activity / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 3'-5'-RNA exonuclease activity / sequence-specific DNA binding / mitochondrial matrix / protein-containing complex / mitochondrion / RNA binding
Similarity search - Function
DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Tetratricopeptide-like helical domain superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSchwinghammer, K. / Cheung, A. / Morozov, Y. / Agaronyan, K. / Temiakov, D. / Cramer, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of Human Mitochondrial RNA Polymerase Elongation Complex
Authors: Schwinghammer, K. / Cheung, A.C.M. / Morozov, Y.I. / Agaronyan, K. / Temiakov, D. / Cramer, P.
History
DepositionMay 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 16, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL
N: 5'-D(*CP*AP*TP*GP*GP*GP*GP*TP*AP*AP*TP*TP*AP*TP *TP*TP*CP*GP*AP*CP*GP*CP*CP*AP*GP*AP*CP*G)-3'
R: 5'-R(*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP)-3'
T: 5'-D(*CP*GP*TP*CP*TP*GP*GP*CP*GP*TP*GP*CP*GP*CP *GP*CP*CP*GP*CP*TP*AP*CP*CP*CP*CP*AP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)145,0594
Polymers145,0594
Non-polymers00
Water4,396244
1
A: DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL
N: 5'-D(*CP*AP*TP*GP*GP*GP*GP*TP*AP*AP*TP*TP*AP*TP *TP*TP*CP*GP*AP*CP*GP*CP*CP*AP*GP*AP*CP*G)-3'
R: 5'-R(*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP)-3'
T: 5'-D(*CP*GP*TP*CP*TP*GP*GP*CP*GP*TP*GP*CP*GP*CP *GP*CP*CP*GP*CP*TP*AP*CP*CP*CP*CP*AP*TP*G)-3'

A: DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL
N: 5'-D(*CP*AP*TP*GP*GP*GP*GP*TP*AP*AP*TP*TP*AP*TP *TP*TP*CP*GP*AP*CP*GP*CP*CP*AP*GP*AP*CP*G)-3'
R: 5'-R(*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP)-3'
T: 5'-D(*CP*GP*TP*CP*TP*GP*GP*CP*GP*TP*GP*CP*GP*CP *GP*CP*CP*GP*CP*TP*AP*CP*CP*CP*CP*AP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)290,1198
Polymers290,1198
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
Buried area19770 Å2
ΔGint-82.5 kcal/mol
Surface area100200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.190, 225.190, 225.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL / Polymerase / MTRPOL / MITOCHONDRIAL RNA POLYMERASE


Mass: 123384.539 Da / Num. of mol.: 1 / Fragment: RESIDUES 151-1230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O00411, DNA-directed RNA polymerase
#2: DNA chain 5'-D(*CP*AP*TP*GP*GP*GP*GP*TP*AP*AP*TP*TP*AP*TP *TP*TP*CP*GP*AP*CP*GP*CP*CP*AP*GP*AP*CP*G)-3' / DNA NON-TEMPLATE STRAND


Mass: 8645.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: RNA chain 5'-R(*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP)-3' / RNA PRODUCT STRAND


Mass: 4493.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*CP*GP*TP*CP*TP*GP*GP*CP*GP*TP*GP*CP*GP*CP *GP*CP*CP*GP*CP*TP*AP*CP*CP*CP*CP*AP*TP*G)-3' / DNA TEMPLATE STRAND


Mass: 8535.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS TAG FOR PURIFICATION FOR CHAIN A

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7.5
Details: 8% PEG 4000, 200 MM SODIUM ACETATE, 100 MM TRISODIUM CITRATE (PH=5.5), 10% GLYCEROL, 10 MM DTT, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2.65→39.8 Å / Num. obs: 54985 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 20.7 % / Biso Wilson estimate: 90.77 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.9
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SPA

3spa


Resolution: 2.65→39.81 Å / Cor.coef. Fo:Fc: 0.9549 / Cor.coef. Fo:Fc free: 0.9465 / SU R Cruickshank DPI: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.337 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2740 4.98 %RANDOM
Rwork0.1793 ---
obs0.1808 54965 100 %-
Displacement parametersBiso mean: 97.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.415 Å
Refinement stepCycle: LAST / Resolution: 2.65→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7880 1178 0 244 9302
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099388HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0312981HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3104SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1226HARMONIC5
X-RAY DIFFRACTIONt_it9388HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion20.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1179SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10470SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2552 200 4.97 %
Rwork0.2232 3822 -
all0.2248 4022 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12152.06271.24176.9091.56323.37530.0279-0.15660.1844-0.9316-0.11.31260.2334-0.54780.07210.4007-0.05780.0271-0.02490.06450.302734.6558200.41787.9426
20.6907-0.80760.04282.4587-1.02531.37250.05060.0901-0.0626-0.2499-0.1953-0.14710.58650.20050.14470.2080.06450.128-0.09070.078-0.015852.7399225.32180.8777
31.179-0.86810.08272.0306-1.63932.7417-0.0871-0.1255-0.00240.2058-0.0464-0.03230.36660.15810.13340.30780.02040.1236-0.05570.08830.082849.417230.39790.1353
41.1035-0.5090.28751.85330.22331.6111-0.1064-0.1283-0.01380.0256-0.09990.17850.0782-0.35570.2063-0.06930.00360.0672-0.04060.0885-0.132937.1507254.41278.4567
54.33461.90572.642613.9061-1.38637.3147-0.13360.3080.1646-0.25680.1651-0.5938-0.4610.578-0.03150.3781-0.2143-0.153-0.09850.19540.019963.6456248.658118.973
67.59286.8359-3.256412.6239-2.878720.0632-0.2504-0.4543-0.6660.7904-0.04950.30210.287-0.5090.2999-0.1346-0.1290.45590.75510.14660.052218.7199251.941107.704
77.18732.20643.41684.9664-3.428410.2072-0.05770.175-0.32770.5811-0.01090.2348-0.1565-0.31220.06860.1180.21970.0512-0.09520.1176-0.031243.382250.52793.012
82.6925-0.611.85453.4489-0.11175.31830.2902-0.41340.03611.3312-0.16630.26340.2292-0.6949-0.1240.3003-0.09130.184-0.12610.2263-0.258639.7004248.973105.973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|218 - A|354 }
2X-RAY DIFFRACTION2{ A|355 - A|548 }
3X-RAY DIFFRACTION3{ A|549 - A|689 }
4X-RAY DIFFRACTION4{ A|690 - A|1230 }
5X-RAY DIFFRACTION5{ N|-26 - N|-18 }
6X-RAY DIFFRACTION6{ N|-11 - N|0 }
7X-RAY DIFFRACTION7{ R|1 - R|9 }
8X-RAY DIFFRACTION8{ T|-9 - T|17 }

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